The global Microcystis interactome

The genetic and ecophysiological diversity of Microcystis

Microcystis is a cyanobacterium that forms toxic blooms in freshwater ecosystems around the world. Biological variation among taxa within the genus is apparent through genetic and phenotypic differences between strains and via the spatial and temporal distribution of strains in the environment, and this fine-scale diversity exerts strong influence over bloom toxicity. Yet we do not know how varying traits of Microcystis strains govern their environmental distribution, the tradeoffs and links between these traits, or how they are encoded at the genomic level. Here we synthesize current knowledge on the importance of diversity within Microcystis and on the genes and traits that likely underpin ecological differentiation of taxa. We briefly review spatial and environmental patterns of Microcystis diversity in the field and genetic evidence for cohesive groups within Microcystis. We then compile data on strain-level diversity regarding growth responses to environmental conditions and explore evidence for variation of community interactions across Microcystis strains. Potential links and tradeoffs between traits are identified and discussed. The resulting picture, while incomplete, highlights key knowledge gaps that need to be filled to enable new models for predicting strain-level dynamics, which influence the development, toxicity and cosmopolitan nature of Microcystis blooms.

Individual Microcystis colonies harbour distinct bacterial communities that differ by Microcystis oligotype and with time

Interactions between bacteria and phytoplankton in the phycosphere have impacts at the scale of whole ecosystems, including the development of harmful algal blooms. The cyanobacterium Microcystis causes toxic blooms that threaten freshwater ecosystems and human health globally. Microcystis grows in colonies that harbour dense assemblages of other bacteria, yet the taxonomic composition of these phycosphere communities and the nature of their interactions with Microcystis are not well characterized. To identify the taxa and compositional variance within Microcystis phycosphere communities, we performed 16S rRNA V4 region amplicon sequencing on individual Microcystis colonies collected biweekly via high-throughput droplet encapsulation during a western Lake Erie cyanobacterial bloom. The Microcystis phycosphere communities were distinct from microbial communities in whole water and bulk phytoplankton seston in western Lake Erie but lacked 'core' taxa found across all colonies. However, dissimilarity in phycosphere community composition correlated with sampling date and the Microcystis 16S rRNA oligotype. Several taxa in the phycosphere were specific to and conserved with Microcystis of a single oligotype or sampling date. Together, this suggests that physiological differences between Microcystis strains, temporal changes in strain phenotypes, and the composition of seeding communities may impact community composition of the Microcystis phycosphere.

Microfluidic and mathematical modeling of aquatic microbial communities

Aquatic microbial communities contribute fundamentally to biogeochemical transformations in natural ecosystems, and disruption of these communities can lead to ecological disasters such as harmful algal blooms. Microbial communities are highly dynamic, and their composition and function are tightly controlled by the biophysical (e.g., light, fluid flow, and temperature) and biochemical (e.g., chemical gradients and cell concentration) parameters of the surrounding environment. Due to the large number of environmental factors involved, a systematic understanding of the microbial community-environment interactions is lacking. In this article, we show that microfluidic platforms present a unique opportunity to recreate well-defined environmental factors in a laboratory setting in a high throughput way, enabling quantitative studies of microbial communities that are amenable to theoretical modeling. The focus of this article is on aquatic microbial communities, but the microfluidic and mathematical models discussed here can be readily applied to investigate other microbiomes.

Dynamics of microcystins and saxitoxin in the Indian River Lagoon, Florida

Harmful algal blooms that can produce toxins are common in the Indian River Lagoon (IRL), which covers ~250 km of Florida's east coast. The current study assessed the dynamics of microcystins and saxitoxin in six segments of the IRL: Banana River Lagoon (BRL), Mosquito Lagoon (ML), Northern IRL (NIRL), Central IRL (CIRL), Southern IRL (SIRL), and the St. Lucie Estuary (SLE). Surface water samples (n = 40) collected during the 2018 wet and 2019 dry season were analyzed to determine associations between toxins and temperature, salinity, pH, oxygen saturation, concentrations of dissolved nutrients and chlorophyll-a, presence of biosynthetic genes for toxins, relative abundance of planktonic species, and composition of the microbial community. The potential toxicity of samples was assessed using multiple mammalian cell lines. Enzyme-Linked Immunosorbent Assays were used to determine concentrations of microcystins and saxitoxin. Overall, the microcystins concentration ranged between 0.01-85.70 µg/L, and saxitoxin concentrations ranged between 0.01-2.43 µg/L across the IRL. Microcystins concentrations were 65% below the limit of quantification (0.05 µg/L), and saxitoxin concentrations were 85% below the limit of detection (0.02 µg/L). Microcystins concentrations were higher in the SLE, while saxitoxin was elevated in the NIRL and BRL. Cytotoxicity related to the presence of microcystins was seen in the SLE during the wet season. No significant patterns between cytotoxicity and saxitoxin were identified. Dissolved nutrients were identified as the most highly related parameters, explaining 53% of microcystin and 47% of saxitoxin variability. Multivariate models suggested cyanobacteria, flagellates, ciliates, and diatoms as the subset of microorganisms whose abundances were maximally correlated with saxitoxin and microcystins concentrations. Lastly, biosynthetic genes for microcystins were detected in the SLE and for saxitoxin in the BRL and NIRL. These results highlight the synergistic roles environmental and biological parameters play in influencing the dynamics of toxin production by harmful algae in the IRL.

Characteristics and bacterial community dynamics during extracellular polymeric substance (EPS) degradation of cyanobacterial blooms

Extracellular polymeric substances (EPSs), which composed of different organic components, play an important role in the formation of mucilaginous cyanobacterial bloom. However, how the phylogeny of microbial community coupling with the degradation of EPS matrixes remains unclear. A better understanding of the dynamic process not only give insight into the carbon cycling in the phycosphere, but also provide a new approach for controlling the cyanobacteria bloom. In this study, fractionated EPSs were prepared as a carbon source to enrich different particle size microorganisms. Changes of organic components in EPSs and microbial communities in the degradation process were investigated using Fluorescence excitation and emission matrix (EEM) and Illumina sequencing. The results showed that it is the change of organic components in the degradation process that causes the microbial community to follow a certain succession law. Size-fractionated microorganisms exhibited different hydrolytic activities when interacting with macromolecules, but they did not present different phylogenetic compositions. The changes of humic-like C1 and tryptophan-like C3 in EPSs were significantly correlated to the variations of microbial community composition and diversity. Tightly-bound EPSs (TB-EPSs) contained more low molecular single carbon compounds and were more easily utilized by more diverse microorganisms. Betaproteobacteria, Firmicute, Alphaproteobacteria, Sphingobacteria and Actinobacter were significantly correlated with the changes of organic maters through the humification process. Meanwhile, loosely-bound EPSs (LB-EPSs), which composed of more macromolecules, were more affiliated to a functional organized microbial community. When Gammaproteobacteria and Betaproteobacteria were involved in LB-EPS degradation as indicators, the polysaccharide structures changed dramatically. And the content of some small molecules was briefly increased during the degradation process. Therefore, in order to prevent algal bloom from reducing cellular aggregation by decreasing viscous EPSs, specialized microbial communities should be considered in the phycosphere.

The involvement of α-proteobacteria Phenylobacterium in maintaining the dominance of toxic Microcystis blooms in Lake Taihu, China

Lake Taihu in China has suffered serious harmful cyanobacterial blooms for decades. The algal blooms threaten the ecological sustainability, drinking water safety, and human health. Although the roles of abiotic factors (such as water temperature and nutrient loading) in promoting Microcystis blooms have been well studied, the importance of biotic factors (e.g. bacterial community) in promoting and meditating Microcystis blooms remains unclear. In this study, we investigated the ecological dynamics of bacterial community, the ratio of toxic Microcystis, as well as microcystin in Lake Taihu. High-throughput 16S rRNA sequencing and principal component analysis (PCA) revealed that the bacteria community compositions (BCCs) clustered into three groups, the partitioning of which corresponded to that of groups according to the toxic profiles (the ratio of toxic Microcystis to total Microcystis, and the microcystin concentrations) of the samples. Further Spearman's correlation network showed that the α-proteobacteria Phenylobacterium strongly positively correlated with the toxic profiles. Subsequent laboratory chemostats experiments demonstrated that three Phenylobacterium strains promoted the dominance of the toxic Microcystis aeruginosa PCC7806 when co-culturing with the non-toxic PCC7806 mcyB^- mutant. Taken together, our data suggested that the α-proteobacteria Phenylobacterium may play a vital role in the maintenance of toxic Microcystis dominance in Lake Taihu.

Genotype and host microbiome alter competitive interactions between Microcystis aeruginosa and Chlorella sorokiniana

Cyanobacterial harmful algal blooms (cyanoHABs) continue to increase in frequency and magnitude, threatening global freshwater ecosystems and services. In north-temperate lakes cyanobacteria appear in early summer, succeeding green algae as the dominant phytoplankton group, a pattern thought to be mediated by changes in temperature and bioavailable nutrients. To understand additional drivers of this successional pattern our study used reciprocal invasion experiments to examine the competitive interaction between Microcystis aeruginosa, a dominant contributor to cyanoHABs, and the green alga Chlorella sorokiniana. We considered two factors that may impact these interactions: (1) strain variation, with a specific emphasis on the presence or absence of the gene for the hepatotoxin microcystin, and (2) host-associated bacteria. We used toxic M. aeruginosa PCC 7806 (microcystin producing strain), a non-toxic mutant of PCC 7806, non-toxic M. aeruginosa PCC 9701 (non-microcystin producing strain), and C. sorokiniana. Each organism was available free of all bacteria (i.e., axenic) and with a re-introduced defined bacterial community to generate their xenic counterparts. Competitive interactions were assessed with reciprocal invasion experiments between paired xenic and paired axenic populations of C. sorokiniana and one of the two Microcystis strains, each assessed separately. Flow cytometry and random forest models were used to rapidly discriminate and quantify phytoplankton population densities with 99% accuracy. We found that M. aeruginosa PCC 7806, but not strain PCC 9701, could proliferate from low abundance in a steady-state population of C. sorokiniana. Further, the presence of bacteria allowed M. aeruginosa PCC 7806 to grow to a higher population density into an established C. sorokiniana population than when grown axenic. Conversely, when M. aeruginosa was dominant, C. sorokiniana was only able to proliferate from low density into the PCC 9701 strain, and only when axenic. The mutant of PCC 7806 lacking the ability to produce microcystin behaved similarly to the toxic wild-type, implying microcystin is not responsible for the difference in competitive abilities observed between the two wild-type strains. Quantification of microcystins (MCs) when PCC 7806 M. aeruginosa was introduced into the C. sorokiniana culture showed two-fold more MCs per cell when host-associated bacteria were absent compared to present in both species cultures. Our results show that the ability of M. aeruginosa to compete with C. sorokiniana is determined by genomic differences beyond genes involved in microcystin toxin generation and indicate an important role of host-associated bacteria in mediating phytoplankton interspecies interactions. These results expand our understanding of the key drivers of phytoplankton succession and the establishment and persistence of freshwater harmful cyanobacterial blooms.

Connections and Feedback: Aquatic, Plant, and Soil Microbiomes in Heterogeneous and Changing Environments

Plant, soil, and aquatic microbiomes interact, but scientists often study them independently. Integrating knowledge across these traditionally separate subdisciplines will generate better understanding of microbial ecological properties. Interactions among plant, soil, and aquatic microbiomes, as well as anthropogenic factors, influence important ecosystem processes, including greenhouse gas fluxes, crop production, nonnative species control, and nutrient flux from terrestrial to aquatic habitats. Terrestrial microbiomes influence nutrient retention and particle movement, thereby influencing the composition and functioning of aquatic microbiomes, which, themselves, govern water quality, and the potential for harmful algal blooms. Understanding how microbiomes drive links among terrestrial (plant and soil) and aquatic habitats will inform management decisions influencing ecosystem services. In the present article, we synthesize knowledge of microbiomes from traditionally disparate fields and how they mediate connections across physically separated systems. We identify knowledge gaps currently limiting our abilities to actualize microbiome management approaches for addressing environmental problems and optimize ecosystem services.